#include "sequence.hpp"
#include "listvector.hpp"
+
+//**********************************************************************************************************************
+vector<string> ListSeqsCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(palignreport);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ListSeqsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The list.seqs command reads a fasta, name, group, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n";
+ helpString += "The list.seqs command parameters are fasta, name, group, list, taxonomy and alignreport. You must provide one of these parameters.\n";
+ helpString += "The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n";
+ helpString += "Example list.seqs(fasta=amazon.fasta).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+ListSeqsCommand::ListSeqsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
ListSeqsCommand::ListSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
}
//**********************************************************************************************************************
-void ListSeqsCommand::help(){
- try {
- m->mothurOut("The list.seqs command reads a fasta, name, group, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n");
- m->mothurOut("The list.seqs command parameters are fasta, name, group, list, taxonomy and alignreport. You must provide one of these parameters.\n");
- m->mothurOut("The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n");
- m->mothurOut("Example list.seqs(fasta=amazon.fasta).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "ListSeqsCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
int ListSeqsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//read functions fill names vector
if (fastafile != "") { inputFileName = fastafile; readFasta(); }
else if (listfile != "") { inputFileName = listfile; readList(); }
else if (taxfile != "") { inputFileName = taxfile; readTax(); }
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { outputTypes.clear(); return 0; }
//sort in alphabetical order
sort(names.begin(), names.end());
ofstream out;
m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
//output to .accnos file
for (int i = 0; i < names.size(); i++) {
- if (m->control_pressed) { out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
out << names[i] << endl;
}
out.close();
- if (m->control_pressed) { remove(outputFileName.c_str()); return 0; }
-
+ if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; }
+
+ m->setAccnosFile(outputFileName);
+
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
m->mothurOut(outputFileName); m->mothurOutEndLine();
m->mothurOutEndLine();
+ //set accnos file as new current accnosfile
+ string current = "";
+ itTypes = outputTypes.find("accnos");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+ }
+
return 0;
}
if (m->control_pressed) { in.close(); return 0; }
- in >> name; //read from first column
+ in >> name; m->gobble(in); //read from first column
in >> group; //read from second column
names.push_back(name);
names.push_back(firstCol);
m->gobble(in);
+
}
in.close();
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